The Japanese capital's troubled preparations for the summer Olympics, especially the soaring costs, will be the major challenge facing the winner.
Euphoria in 2013 at securing the right to host sport's marquee event has given way to frustration over gaffes and scandals.
A record 21 candidates are vying to lead the metropolis with a total population of 13.6 million and an economy the size of Indonesia's.
Local media surveys, however, suggest it is a three-way race between former defence minister Yuriko Koike, former governor of the northeastern prefecture of Iwate Hiroya Masuda and veteran TV journalist Shuntaro Torigoe.
Vote-counting begins immediately after polls close at 8 pm.
The election was called after governor Yoichi Masuzoe abruptly resigned, felled by a scandal over his lavish spending of public money. He served just over half his term.
His predecessor Naoki Inose -- who had led the successful bid to win the Games -- bowed out later in 2013 after becoming embroiled in a personal financial scandal, serving just one year.
Koike, a 64-year-old former TV anchorwoman, speaks fluent English and Arabic -- the latter acquired as a student in Cairo -- and has also served as environment minister.
Masuda, also 64 and backed by Abe's LDP-led ruling coalition -- which spurned Koike for not seeking its approval before announcing her candidacy -- is a veteran administrator who won plaudits as governor of Iwate for 12 years until 2007.
Torigoe, 76, is a liberal journalist widely known in Japan for his ubiquitous TV appearances and also as a cancer survivor.
The winner's four-year term will extend until just after the Games start and the governor's performance in the run-up will be closely watched.
The Tokyo Games have also been hit by one embarrassment after another.
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